Signals of selection

Signals of selection

Per Unneberg

NBIS

12/13/22

Selection

Topics

  • direct selection(?)

Linked selection

Tajima’s D

Selective sweep

Use (Figure 2 Charlesworth & Jensen, 2021)

Selective sweep

Code 
pgip-slim --seed 42 -n 1000 -r 1e-6 -m 1e-7 --threads 12 recipes/slim/selective_sweep.slim -l 1000000 --outdir results/slim
pgip-tsstat results/slim/slim*.trees -n 10 --seed 31 -s pi -s S -s TajD -w 500 --threads 10 | gzip -v - > results/slim/selective_sweep.w500.csv.gz

The effect of a selective sweep on different statistics.

Selective sweep

Code 
pgip-slim --seed 42 -n 1000 -r 1e-6 -m 1e-7 --threads 12 recipes/slim/selective_sweep.slim -l 1000000 --outdir results/slim
pgip-tsstat results/slim/slim*.trees -n 10 --seed 31 -s pi -s S -s TajD -w 500 --threads 10 | gzip -v - > results/slim/selective_sweep.w500.csv.gz

The effect of a selective sweep on different statistics.

References

Signals of selection

Charlesworth, B., & Jensen, J. D. (2021). Effects of selection at linked sites on patterns of genetic variability. Annual Review of Ecology, Evolution, and Systematics, 52(1), 177–197. https://doi.org/10.1146/annurev-ecolsys-010621-044528
Nielsen, R. (2005). Molecular Signatures of Natural Selection. Annual Review of Genetics, 39(1), 197–218. https://doi.org/10.1146/annurev.genet.39.073003.112420